X!TandemPipeline is a free software (GPL v3) that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

A full description of X!TandemPipeline has been published in:

Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503

main features

graphical user interface

grouping algorithm

Our grouping algorithm removes non informative redundant informations from your dataset and builds clusters of proteins (groups and subgroups). Redundancy of protein databases is fully filtered as follows :

  • proteins identified without specific peptides compared to others are eliminated
  • proteins identified with the same pool of peptides are assembled (subgroups)
  • proteins are grouped by functions (identified with at least one common peptide), and the specific peptides for each sub-group of proteins are highlighted


X!TandemPipeline (C++) was developped to be fast, with a low memory footprint. For example, given a common dataset :

  • 12 complex biological samples (iPRG 2015 study)
  • corresponding to 2619 identified proteins, 24548 unique peptides
  • and 193657 MS/MS spectrums

would give on a basic computer (1,4Go RAM, 3Ghz CPU) :

  • 2419 groups of proteins (same protein function, at least one common peptide)
  • 2586 subgroups of proteins (each protein sharing the same set of peptides)
  • 59 seconds total runtime to read, filter and group the 12 MS identification files (X!Tandem XML files)
  • 1 second only to filter and group


Many thanks to the Global Proteome Machine organisation (the GPM) that develops the X!Tandem free search engine software. Many thanks to [SourceSup] (https://sourcesup.renater.fr/projects/xtandempipeline/), for effectively hosting the X!TandemPipeline (C++) project.